Reading this thread:
https://bg.battletech.com/forums/total-warfare/physical-attacks-against-quad-mechs-in-depth-1-water/the threads linked in it, and BMM (pp. 26, 35, 64-65), TW (pp. 102, 107-108, 144), and AGoAC rulebook (pp. 17, 19 and 25) leads me to believe that there are a few problems with the rules regarding physical combat. Most of the problems seem to occur during combat between 'Mechs standing in Depth 1 water.
1. Kick Attacks. According to p. 35 BMM "For a standing biped ’Mech, Depth 1 water provides partial cover against any physical attack that does not roll on the Punch Location Table [...]", which would mean that a kick attack between two 'Mechs standing in Depth 1 water would be subjected to a +1 to-hit penalty for partial cover. One of the old rules answers (
https://bg.battletech.com/forums/total-warfare/answered-bmm-water-providing-or-not-providing-cover-to-physical-attacks) and p. 25 of the AGoAC rulebook explicitly disagree - according to them the attacking 'Mech to-hit penalty. As far as I can tell TW does not address this situation explicitly, but the general rules for partial cover in this book are written in such way, that I think that according to TW the attack would qualify for a +1 to-hit modifier.
So I guess we need corrections in at least one book to cover this case (my guess is BMM, and possibly TW)?
At least all sources seem to agree here that a successful kick would deal half of the standard damage (rounded down)...
2. Physical Weapon and charge attacks. Even worse, the following paragraph p. 35 BMM reads "If partial cover applies, resolve the physical attack’s hit location as normal. However, if the attacker is at Level 0, any damage grouping that resolves to the legs is ignored. If the attacker is instead in water of Depth 1 or deeper, any damage grouping that resolves to any location except the legs is ignored.", which would mean that a physical attack that uses regular Hit Location Table (like a charge or most physical weapon attacks) would not only suffer a +1 to-hit, but
all damage groupings from such attacks that did not hit target's legs would be ignored, which doesn't make sense to me. According to p. 25 AGoAC rulebook such attacks would suffer a +1 to-hit penalty, but unlike BMM would be able to damage any part of a 'Mech
except legs (which seems fine for physical weapon attacks, but not necessarily for charge attacks). Same thing seems to be the case under TW rules.
Which rules (if any) are correct here? My guess would be that charge attacks shouldn't suffer any penalties for partial cover (no +1 to-hit modifier, no damage groupings striking cover instead of target 'Mech (or the attacking 'Mech)), while physical weapon attacks that use regular Hit Location Table should suffer typical penalties for partial cover (+1 to-hit, and all damage groupings to the legs ignored).
3. Amount of damage dealt. The rules in all books are also unclear about amount of damage that would be dealt in such situation - would such attacks be considered as "beginning under water", which would mean the damage from it is halved (see pp. 35, 65 BMM, 144 TW), or not? For physical weapon attacks I would guess "not", but I wouldn't be so sure about charge attacks, though at the same time I think that damage from underwater charge attacks probably shouldn't be halved regardless of depth at which they happen, since in case of 'Mechs the increased MP cost for moving them through water already reduces damage potential of such attacks, while at the same time I fail to see a reason to halve charge attack damage from units that can actually move quickly on or under water (like naval vessels or hovercraft) compared to charge attack damage done by units with the same mass moving at the same speed outside of water. Another problem with halving damage from charge attacks is that it rises additional questions not covered by the rules, like "Is damage to the attacker also halved?" or "Is only the damage to the legs, not torso, head or arms, halved?"
4. Attacks from Depth 2. Finally there is a case where a 'Mech standing at depth 2 attacks a 'Mech standing at depth 1 (assuming that water surface at both adjacent hexes is at the same level). According to Different Levels Table (pp. 34 BMM, 150 TW, 25 AGoAC rulebook) all physical attacks possible in this situation (except charge) use Kick Table, which according to all three rulebooks would mean that the target 'Mech would get partial cover, the damage from attacks would be halved, and could only strike the legs. The only problematic attack is a charge - according to p. 26, 35 BMM, 108 TW, (but not according to AGoAC rulebook) any damage from such charge attacks striking any part of the 'Mech other than legs would be ignored. Doesn't seem logical to me for reasons similar to the ones I've mentioned in point 2., especially since Different Levels Table instructs players to use regular Hit Location Table regardless of which 'Mech (if any) is standing higher prior to attack, which makes me think that the rules' intent is that charge attacks should be resolved as if the attacker entered the target's hex (and, as a consequence -
level)
first, and only
aferwards collided with the target.
5. Quick reccomendation. Aside from the changes suggested in the previous points, I think that the sentence "If the attacker is instead in water of Depth 1 or deeper, any damage grouping that resolves to any location except the legs is ignored." on p. 35 BMM should be scratched from the book, because if both the attacker and the target are on Depth 1 I see no reason why physical attacks other than kicks wouldn't be able to hit 'Mech locations other than legs (if anything it is the legs that IMO should be protected from some attacks - as discussed above), and if the attacker is at Depth 2 all possible physical attacks other that charges may only hit target's legs anyway because they use Kick Table to resolve hit locations, while charge attacks should be able to hit any part of target 'Mech anyway. So in every possible case the sentence in question is either wrong or redundant.
By the way on official maps water level on two adjacent hexes isn't always at the same level (see Large Mountain #1 and LOS diagrams derived from it - pp. 100 TW, 23 BMM, 14 AGoAC rulebook), - a situation which comes with its own problems when resolving physical attacks, but I think that we can leave these for another thread.

There is also another small issue that I noticed while working on this post - "Water" paragraph in Partial Cover Modifier section of p. 26 BMM is worded in such way that it may suggest that attacks striking Torso, Head or Legs of a 'Mech standing in Depth 1 water strike cover instead only if they are made by a fully submerged 'Mech, which aside from all problems with physical attacks mentioned above isn't even always true for weapon attacks - leg mounted weapon attacks are resolved like that even when they are fired by partially submerged 'Mech. This case is explained on p. 64 BMM, but should probably be also mentioned on p. 26 BMM.